Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
0
votes
1
reply
2.6k
views
Comment: C: How to create vcf file with SNPs bed file and sorted bam file?
4.8 years ago by O.rka ▴ 750
0
votes
1
reply
2.6k
views
Comment: C: How to create vcf file with SNPs bed file and sorted bam file?
4.8 years ago by O.rka ▴ 750
1
vote
7
replies
2.6k
views
How to create vcf file with SNPs bed file and sorted bam file?
RNA-Seq genome variant
updated 4.8 years ago by ▴ 180 • written 4.8 years ago by ▴ 750
0
votes
0
replies
2.6k
views
Comment: C: How to create vcf file with SNPs bed file and sorted bam file?
4.8 years ago by O.rka ▴ 750
0
votes
0
replies
4.5k
views
Comment: C: metabat installation problem with conda
4.8 years ago by O.rka ▴ 750
0
votes
1
reply
1.0k
views
Can I use metatranscriptomic reads for coverage when doing metagenomic binning?
metagenomics metatranscriptomics binning
updated 4.8 years ago by ★ 30k • written 4.8 years ago by ▴ 750
1
vote
0
replies
4.2k
views
Answer: A: EC number regular expression
4.9 years ago by O.rka ▴ 750
1
vote
1
reply
1.7k
views
How to look for enrichment of pathways using a list of EC numbers (enzyme)?
enzyme enrichment gsea picrust gene set
4.9 years ago by O.rka ▴ 750
6
votes
6
replies
8.5k
views
Is it possible to get taxonomy identifiers from diamond output without using --taxonmap during makedb?
diamond blast protein alignment taxonomy
updated 23 months ago by ▴ 30 • written 5.8 years ago by ▴ 750
0
votes
1
reply
2.3k
views
What is an easy-to-use `conda` installable method for annotating proteins for eukaryotes?
annotation genome proteins eukaryotes
updated 5.1 years ago by ★ 30k • written 5.1 years ago by ▴ 750
0
votes
2
replies
2.1k
views
How to find all mapped locations of a read from PySam?
alignment
updated 5.1 years ago by 12k • written 5.1 years ago by ▴ 750
0
votes
0
replies
2.1k
views
Comment: C: How to find all mapped locations of a read from PySam?
5.1 years ago by O.rka ▴ 750
0
votes
0
replies
988
views
What does it mean when "-" or "+" join KEGG orthologs in a KEGG module definition?
kegg ortholog module annotation metagenomics
5.5 years ago by O.rka ▴ 750
0
votes
0
replies
3.2k
views
Comment: C: Why is hmmsearch only using the 1st HMM in a concatenated HMM database?
5.5 years ago by O.rka ▴ 750
0
votes
1
reply
3.2k
views
Comment: C: Why is hmmsearch only using the 1st HMM in a concatenated HMM database?
5.5 years ago by O.rka ▴ 750
2
votes
4
replies
3.2k
views
Why is hmmsearch only using the 1st HMM in a concatenated HMM database?
hmm hmmer protein domain bash script
updated 5.5 years ago by ★ 30k • written 5.5 years ago by ▴ 750
0
votes
1
reply
6.9k
views
Comment: C: How to choose between --cut_ga, --cut_tc, and --cut_nc in hmmsearch? (hmmer)
5.5 years ago by O.rka ▴ 750
0
votes
1
reply
6.9k
views
Comment: C: How to choose between --cut_ga, --cut_tc, and --cut_nc in hmmsearch? (hmmer)
5.5 years ago by O.rka ▴ 750
0
votes
1
reply
6.9k
views
Comment: C: How to choose between --cut_ga, --cut_tc, and --cut_nc in hmmsearch? (hmmer)
5.5 years ago by O.rka ▴ 750
4
votes
7
replies
6.9k
views
How to choose between --cut_ga, --cut_tc, and --cut_nc in hmmsearch? (hmmer)
alignment hmm protein domain
updated 5.5 years ago by ★ 30k • written 5.5 years ago by ▴ 750
0
votes
0
replies
702
views
How should I handle mapping to incomplete genome with many homologous regions?
RNA-Seq
updated 5.5 years ago by 20 • written 5.5 years ago by ▴ 750
0
votes
0
replies
1.4k
views
Comment: C: How to get "best" taxon identifier from diamond output with staxids?
5.5 years ago by O.rka ▴ 750
0
votes
0
replies
4.4k
views
Comment: C: BLAST multiple staxids
5.5 years ago by O.rka ▴ 750
0
votes
2
replies
1.4k
views
How to get "best" taxon identifier from diamond output with staxids?
metagenomics blast diamond alignment protein
5.5 years ago by O.rka ▴ 750
0
votes
1
reply
4.5k
views
Comment: C: How can I get taxonomy identifiers (staxids) using diamond? (Error: Invalid outp
5.5 years ago by O.rka ▴ 750
2
votes
3
replies
4.5k
views
How can I get taxonomy identifiers (staxids) using diamond? (Error: Invalid output format. Allowed values: 0,5,6,100,101,102)
alignment diamond
updated 5.5 years ago by 166k • written 5.5 years ago by ▴ 750
0
votes
0
replies
17k
views
Comment: C: nr database Diamond
5.5 years ago by O.rka ▴ 750
0
votes
2
replies
1.8k
views
What are recommended parameters for removing rRNA from meta[transcript][gen]omics using bbduk.sh?
RNA-Seq metagenomics
5.5 years ago by O.rka ▴ 750
0
votes
0
replies
2.9k
views
Comment: C: How can I transfer gene models to a new assembly?
5.5 years ago by O.rka ▴ 750
0
votes
0
replies
2.9k
views
Comment: C: How can I transfer gene models to a new assembly?
5.5 years ago by O.rka ▴ 750
0
votes
0
replies
2.9k
views
Comment: C: How can I transfer gene models to a new assembly?
5.5 years ago by O.rka ▴ 750
2
votes
5
replies
1.0k
views
If you generate a main text figure in a publication, does that deserve coauthorship?
academia
updated 5.5 years ago by ★ 30k • written 5.5 years ago by ▴ 750
0
votes
0
replies
8.5k
views
Comment: C: Is it possible to get taxonomy identifiers from diamond output without using --t
5.6 years ago by O.rka ▴ 750
0
votes
0
replies
12k
views
Comment: C: Why is `send` lower than `sstart` from blast format 6 output?
5.6 years ago by O.rka ▴ 750
0
votes
0
replies
1.6k
views
Comment: C: Is there a tool for calculating the number of uniquely mapped reads, ambigiously
5.6 years ago by O.rka ▴ 750
0
votes
0
replies
1.6k
views
Comment: C: Is there a tool for calculating the number of uniquely mapped reads, ambigiously
5.6 years ago by O.rka ▴ 750
1
vote
5
replies
1.6k
views
Is there a tool for calculating the number of uniquely mapped reads, ambigiously mapped reads, and unmapped reads from sam/bam?
RNA-Seq
5.6 years ago by O.rka ▴ 750
0
votes
0
replies
52k
views
Comment: C: Fast download of FASTQ files from the European Nucleotide Archive (ENA)
5.7 years ago by O.rka ▴ 750
0
votes
1
reply
2.1k
views
Comment: C: Does fastq dump return interleaved files?
5.7 years ago by O.rka ▴ 750
0
votes
7
replies
2.1k
views
Does fastq dump return interleaved files?
sequence
updated 5.7 years ago by 89k • written 5.7 years ago by ▴ 750
0
votes
1
reply
2.8k
views
Basic fasterq-dump command is failing from `SIGNAL - Segmentation fault`
sequencing
updated 5.7 years ago by 89k • written 5.7 years ago by ▴ 750
5
votes
2
replies
2.8k
views
Remove duplicate reads before variant calling?
snp
updated 5.7 years ago by 22k • written 5.7 years ago by ▴ 750
0
votes
1
reply
2.5k
views
Comment: C: How do I know how much memory to use when piping to with BBMap suite (OutOfMemor
5.7 years ago by O.rka ▴ 750
4
votes
3
replies
2.5k
views
How do I know how much memory to use when piping to with BBMap suite (OutOfMemoryError)?
bbmap java memory reads
updated 22 months ago by 20k • written 5.7 years ago by ▴ 750
0
votes
0
replies
24k
views
Comment: C: What Does The Zero Mapping Quality Mean For The Bwa Mapper?
5.8 years ago by O.rka ▴ 750
1
vote
0
replies
1.2k
views
Answer: A: How to use ENCprime via coRdon with a custom background sequence set?
5.8 years ago by O.rka ▴ 750
2
votes
1
reply
1.2k
views
How to use ENCprime via coRdon with a custom background sequence set?
gene Bioconductor R
5.8 years ago by O.rka ▴ 750
2
votes
1
reply
1.1k
views
Is there a method or HMM set to quickly determine if a sequence has a tRNA sequence for a large number of sequences/reads?
trna sequence
updated 5.8 years ago by ★ 30k • written 5.8 years ago by ▴ 750
0
votes
0
replies
895
views
Any alternatives to phylosift for identifying ribosomal proteins from metagenomic reads?
gene ribosomal
5.8 years ago by O.rka ▴ 750
0
votes
0
replies
1.8k
views
Comment: C: How to increase speed of BBMap's `reformat.sh` when randomly sampling reads?
5.8 years ago by O.rka ▴ 750
410 results • Page 5 of 9
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6